Genetics Primer
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Gene Pools
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Regression to Mean



(Published in The Essential Horse - November 1997)

Progress in the field of genetics has been moving by leaps and bounds during the past few years.  It wasn't long ago that researchers discovered ways to unravel and study DNA, that elusive strand of genes that inhabits each and every cell. Once that breakthrough was made, discoveries cane at an almost dizzying pace. Specific genes were identified and located.  Another startling and, to many disturbing, step forward came recently.  Scientist cloned sheep.

What does all this mean to horsemen?  It can and should mean a great deal. By taking advantage of past and present knowledge, we can take steps to produce stronger, healthier horses and steer away from some crippling diseases.

Genetics progress in the horse world has been slower than in other phases of agriculture. There likely are a couple of reasons for that.  Many of the horses in existence are bred strictly for the pleasure of the owners. Beef cattle, hogs, chickens, dairy cows and sheep, however all are creatures that are bred and raised for food and profit.

With profit as an incentive, there has been great genetic progress with animals produced for meat.  For example, one can buy just-hatched baby chicks, put them on the put them on the proper feed program, and eight weeks later pack them into the freezer as four- to five-pound broilers.  With hogs, there has been a complete change in the type of animal produced only a few decades ago. When the consumer complained of too much fat,  the geneticists developed a longer, leaner hog that packed only a small amount of fat on its frame. It has been the same with beef and sheep. Of Course, it is easier to facilitate relatively rapid changes in the chicken and population because of the numbers involved. The number of fertilized chicken eggs with which researchers could work, for example, was basically limitless.  And with hogs, one sow can deliver a dozen offspring at a time.

It isn't the same with horses. If the breeders is lucky, his or her broodmare will produce a single foal each year of her productive life.

The late Daniel Gainey, founder of Jostens Company in Owatonna, Minnesota, and a prominent Arabian breeder for many years, used to put it something like this: "In business, I count on progress by the decade. With horses, it takes longer."

So how does this business of genetics work?  How can we determine which mare to put to which stallion? The answer is both simple and complicated. It is simple because the offspring will receive a set of genes from each parent and they will determine the newcomer's physical and mental makeup.  It is complicated because the deeper we get into the process, the more variable come into play.

It is also complex because it sometime is difficult to differentiate between genetic and environmental factors. Does the colt start chewing on fences because it was genetically predisposed to do so, or did the colt learn to chew from watching its mother. Or is it a combination of both.

It's the same with temperament. Is a particular foal mean-spirited because he inherited those genes, or because its mother has a bad temper and it learned the same through observation?  In this scenario, the problem becomes more complicated if the sire of the foal is a mild-mannered horse.

And how about the differences between full brothers or sister.  One might be large and robust and the other small and lacking in strength. Genetics? Or, was it a difference in feeding programs when the two were young?

How about breeding decisions? If we have a 17-hand mare and want a smaller offspring, what will happen when we breed her to a 13-hand stallion? Will the foal be 15 hands, splitting the difference for each parent, so to speak.

If we breed a fast stallion to a slow mare, will we get an offspring that will have moderate speed?

Because this article is designed to be a primer on genetics, we must start at the beginning of this relatively new science if we are to find some answers to these questions.

Back to Basics

The first realization we must have is that because of the complex nature of our genetics makeup, there is great variation. We need only look around us in a crowded room or in a stadium filled with thousands of people. There might be similarities, but very few will look alike.

Yet, there also are traits that are passed down in families from generation to generation. If one studies photos of the European royalty family Hapsburg, it quickly will become evident that a protruding lower lip shows up in generation after generation, the result of a particular gene being expressed.

When we refer to the field of genetics as a relatively new science, we are being accurate. The father of the study of genetics was an Austrian monk named Gregor Mendel.  He was born in 1822 and died in 1884. We he was conducting his experiments, science did not know of the existence of chromosomes. For Mendel to accomplish what he did without knowledge of chromosomes is truly one of the greatest intellectual accomplishments in the field of science.

Mendel was the son of peasant parents. He was educated in the monastery in Czechoslovakia and from there went to the University of Vienna, where he studied science and mathematics. Then misfortune, or more likely fortune, struck. (It was unfortunate for Mendel at the time, but fortunate of the science of genetics.)  Mendel failed to pass his examination for a teaching certificate. He returned to the monastery and remained there for the rest of his life.

At the monastery Mendel initiated a series of studies aimed at unraveling some of the mysteries of genetics. For his experiments, Mendel selected the common garden pea.

It was a good choice, because garden peas are small plants that are easy to grow, with a short germination time that meant several generations could be produced and studied in a single year.

Studying Mendel's progress with the pea plants can serve to open the door of knowledge on genetics at the basic level because the concepts are  the same, be the subject pea plants or horses.

First, Mendel simply studied the plants that grew in the monastery garden for several generations. He found, for example, that plants with white flowers when fertilized by like plants always produced plants with white flowers, regardless of the number of generations involved. When fertilized with the plants that produced purple flowers. When fertilized by like plants, the new plants always bore purple flowers.

Now for the experiment. The monk decided to produce hybrid plants by crossing purple flowered plants with white flowered plants.  Mendel removed the male part from a plant that produced white flower and fertilized that plant with pollen from a plant that always produced purple flowers. He did the reverse--fertilizing a plant that produced purple plants with pollen from a white-flower plant

At that time, one of the prevailing theories was that if plants with opposing colors were crossed, the result would be a plant that was intermediate in color. In the case of white-flowered plants being crossed with the purple-flowered, the result was expected to be light lavender.

Mendel proved that theory to be groundless. He did not get any plants with intermediate coloration with his crossbreeding program. Remember the question about crossing tall mare with short stallion? The likely result would be that the offspring would basically be either tall or short. This does not mean that the offspring would basically be either short or tall. This does not mean that the offspring would be the exact size of one of the parents. Since one or the other of the genes--tall or short--would be expressed, it is unlikely that the resultant foal would wind up midway between the parents in size.

However, we are getting ahead of ourselves. Back to Mendel and his pea plants.

Mendel found that in each case where he crossed a white flowered plant with a a purple flowered plant, the resultant offspring were all purple. This first generation of plants would be referred to as the first filial or the F1 generation.

Mendel referred to the trait expressed as the color purple as being "dominant." The trait not expressed he referred to as "recessive."  Thus, the purple flowered plant was dominant over the white flowered plant. The terms dominant and recessive have become the most common terms used when discussing genetics.

After the F1 plants with their purple flowers had matured, Mendel allowed them to self pollinate in an effort to see what would happen in the second filial or F2 generation. Then the results were different. Not all of the plants in the second or F2 generation had purple flowers. Some of the flowers were white, meaning that the recessive trait had been latent in the first generation, but now was active.

Mendel discovered something else. The white flower F2 plants always produced white flowers when allowed to self-fertilize. By contrast, only one-third of the purple flowered plants produced offspring with purple flowers, despite the fact that they were dormant. That led to the conclusion that one-fourth of the plants were not pure-breeding dominant individuals; one-fourth were pure breeding recessive individuals.

The 3:1 ratio of dominant over recessive is referred to as the Mendelian ratio.

Armed with the knowledge that these are dominant traits and recessive traits, let's switch our attention to genetics in horse breeding.

Each horse's body contains multitudinous cells. Within each cell is the genetic blueprint for that animal. The blueprint or genetic material is carried on chromosome, which are slender, threadlike structures that are paired. A horse has 64 chromosomes or 32 pairs. At various locations--referred to as loci or locus--on these chromosomes are genes. A gene is comprised of a DNA nucleotide sequence.  Just as is the case with chromosomes, genes exist in pairs. The two genes that are paired are referred to as alleles. However, just because in pairs, doesn't mean the pairs are identical. Often they are not.

If paired genes are identical, the individual is referred to as being homozygous. If the paired genes are not identical, the term used heterozygous.  Homozygous individuals have only one allele to pass on to their offspring. Heterozygous individuals can pass on either of the two different alleles possessed in their genetic makeup.

This passing of traits all occurs at the moment of conception. When the sperm fertilizes the egg, the paired chromosomes from parent split with a single set of 32 chromosomes from each joining pair for a total of 64 individual chromosomes. This means, of course, that there is a new pairing of genes or alleles.

So, now the potential offspring of these two individuals is endowed with a complete set of genes from each parent. The way in which the genes pair up will determine which genes are expressed.

The genetic rule of thumb is that the dominant gene always will have its way when paired with a recessive gene. Sometimes, however, both parents pass on a recessive gene for a particular trait, and it is then that the recessive gene will be expressed.

A case in point. For some years, a particular breed of beef cattle suffered from  dwarfism as a result of a recessive gene. Any time a bull and cow were mated with each carrying the recessive gene ant those genes paired up at the time of fertilization, the recessive gene would be expressed  and the offspring would be a dwarf. Selective breeding that made certain that at least one parent carried a dominant gene for growth has pretty much wiped out the problem.

There are a couple of genetic health problems in particular breeds of horses today that are the result of recessive genes.  More about that later.

First there are two other terms with which we should become acquainted: genotype and phenotype. The phenotype is the outward manifestation of the genes being carried. In other words, the genotype is the blueprint and the phenotype is the realized outcome.

"There are two basic types of genetic action--qualitative and quantitative," writes E.I. Johnson, PhD, of the University of Florida, in a paper on equine genetics. "In qualitative gene action, a particular trait is influenced by a single pair of genes, or maybe two or three pairs of genes. In quantitative gene action, a trait such as speed is influenced by a number of genes that all have some influence on the trait."

"In traits affected by qualitative gene action, there are three primary types of gene action that affect the trait. The types of gene action are dominance, codominance, and partial dominance. Dominance is defined as the ability to mask or cover up its recessive allele. Codominance in gene action results in an intermediate state between the two parents. An example of codominance is blood type.  Each blood type is different and known and thus indicates the genotype. Partial dominance also results in an intermediate state, but not necessarily an exact intermediate state. An example of a partial dominant state is the dilution gene affecting color. The base color, such as bay or sorrel, have no dilution genes.  When one dilution gene is present, the base color is altered (diluted) to buckskin or palomino. If two dilution genes are present, the base color will be diluted to cremello or perlino."

Most traits in horses are influenced by quantitative gene action. A good example would be speed in a Thoroughbred, Quarter Horse, or Standardbred.  there is no single gene that determines speed at which one animal can run.  Instead, multiple genes are involved, with factors like size, sturdiness of leg, heart and lung capacity, coordination, muscle efficiency, strong tendons, ligaments, and joints and mental traits that govern the horse's will to win.

Then, of course, environmental factors become involved. Training and nutrition, for example, can strongly influence how well a horse performs.

Johnson contends that all genetic traits have a heritable estimate:  "The heritability estimate is essentially the percentage of a horse's expressed trait that is due to genetics.  The percentage that is due to genetics indicates the probability of the being passed on from one generation to the next.  Specifically, the heritability estimate of a trait refers to the ability to select horses to mate based on superior performance for the trait and to predict the improvement in the offspring.  Some traits are highly heritable and other are low.  In any selection process, greater progress can be made when keeping the number of traits selected to a minimum."

"If a horse is selected for only one trait, then greater selection pressure (horses more outstanding in that trait) can be applied on that trait.  Selecting for traits that are highly heritable also greatly increase the chance for improvement.  For the traits that have a low heritability estimate, much greater success can be achieved by controlling the environment and management regimes."

Johnson provides these heritability estimates for certain traits in horses.

  • Height at withers--45 to 50

  • Body weight--25 to 30

  • Body length--35 to 40

  • Heart girth circumference--20 to 25

  • Cannon bone circumference--20 to 25

  • Pulling power--20 to 30

  • Running speed--35 to 40

  • Walking speed--40 to 45

  • Trotting speed--35 to 45

  • Movement--40 to 50

  • Temperament--25 to 30

  • Cow sense--Moderate to high

  • Type and conformation--Moderate

  • Reproductive traits--Low

  • Intelligence--Moderate to high

So, one can conclude there are no magic genetic formulas in breeding. The old adage of "breed the best to the best'" has some validity, but it does not guarantee a highly improved offspring.

The great Secretariat is an example. He was one of the mightiest runners ever to set foot on a track, yet few of his offspring even came close to duplicating his performances. Somehow, some to those key quantitative genes involved in racing success were not expressed in his get.

While the goal always should be to improve the offspring, there are far too many breeding programs that breed for only a single trait and forget all the others. Racing is a case in point. Far too many runners which cannot compete because of weaknesses in leg bones, joints, ligaments and tendons are put into the breeding shed and mated with others who cannot compete for the same reason. It doesn't take a Gregor Mendel to determine the probable outcome for such a cross. The colt or filly might inherit blazing speed, but the opportunity to display it likely will be short-lived before the same weakness that ended the careers of the parents will do the same for the offspring.

Unfortunately, genes do not always remain in unaltered form. Sometimes defects occur and when that is the case, certain weakness or diseases are easily passed from one generation to another.

Remember that the entire blueprint for a horse resides in the minuscule amount of DNA found in the nucleus of a single microscopic cell.

Jill J. McClure, D.V.M., MS, of Louisiana State University, used this colorful description to describe DNA: "The DNA consists of a series of genes aligned like the Christmas tree lights on a string."

Defects in the DNA blueprint, she writes, can result in the failure to form essential proteins or the formation of abnormal proteins that can result in death and disease.

Diseases involving DNA, she explained, can be divided into two categories--those that result from mutant genes and those that occur from chromosome aberrations, which are the result of accidental damage to chromosomes during reproduction.

The diseases that result from mutations can be passed from one generation to another. A case in point is combined immunodeficiency (CID), an inherited disease of Arabian and part-0Arabian horses. Foals with the malady are born bereft of a normal immune system and usually die shortly after birth as the result of infections against which their bodies have no defense.

"The defect" reports McClure, " is believed to have arisen originally from a mutation in a single gene in a single individual (point mutation), which was then perpetuated by the intense breeding of the affected line. Some estimates suggest that as many as 25% of Arabians in the United States carry the gene for CID and that  two to three percent of all Arabian foals are born affected."

Two recessive genes are required for CID to be exhibited.  If an Arabian has one dominant gene and one recessive--heterozygous--the dominant gene will prevail, but the will still be a carrier.  If a heterozygous horse is mated to one that is homozygous normal, all the foals will be normal, but half of them would be carriers. In the heterozygous horses, all would be normal, but all also would be carriers.  If two heterozygous horses were mated, the expected outcome would be that 25% would inherit two copies of the normal dominant gene; 50% would be phenotypically normal with one dominant and one recessive gene, but would be carriers, and 25% would inherit two copies of the recessive gene and have CID. 

Hyperkalemic period paralysis (HYPP) is another example of a gene mutation that started with one Quarter Horse stallion, Impressive. The affliction is characterized  by intermittent attacks of muscle tremors, weakness, disorientation, or convulsions. The HYPP gene differs from the CID gene in that the HYPP gene is dominant.  McClure gives this explanation:

"The disease (HYPP) is transmitted by an autosomal dominant mode of inheritance. At least one of the parents of an affected animal must also carry the gene and be affected, but not necessarily both, because this is a dominant condition and only one abnormal gene need be present. The defect is believed to have originated as a point mutation in the gene that controls the protein that regulates the movement of sodium into and out of muscle. Both the normal and abnormal alleles for this gene have been identified. Only one  amino acid is different between the normal and abnormal proteins, emphasizing how even small changes can make significant clinical differences."

Because of the popularity of Impressive and his offspring, it is estimated that approximately 100,000 Quarter Horses carry the gene for HYPP.

HYPP and CID are only two of a number of genetic diseases. When genetics problem stems from chromosome damage or abnormalities, the result is frequently early embryonic death. When there is survival, reports McClure, the horses tend to exhibit growth defects and infertility.  Here is her explanation of chromosome damage:

"During reproduction, the chromosomes of each parent are copied and then packaged individually into germ cells (either sperm or eggs). During the process of copying and packaging, things can go wrong, resulting in chromosomal breakage, deletion, duplication, or misalignment. Chromosomal defects are associated with alterations of either whole or relative large sections of the chromosomes containing many genes."

"They have no consistent mode of inheritance because they are largely the result of sporadic accidents of nature. Chromosomal abnormalities involving large segments of chromosomes and significant numbers of genes are incompatible with life and result in early embryonic death.  this probably explains why manifestation of chromosomal defects in horses that are actually born relatively uncommon."

There is much that is known in the field of equine genetics and much to be learned. Horse owners who stay abreast of the exciting research will discover many benefits that will help them produce a better horse.



Les Sellnow is a free-lance writer specializing in articles on equine research.  Based in Riverton, Wyoming, Sellnow also is author of fiction and non-fiction books.